[ENSWEB-3350] fix jump to region on alignslice view

Author: jyothishnt

htdocs/components/10_ZMenu.js

@@ -54,21 +54,19 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
 
     if (this.drag) {
       params = this.href.split('|');
-      n      = parseInt(params[1], 10) - 1;
-      
+      n                = parseInt(params[1], 10) - 1;
       this.speciesPath = params[3].replace(/-/, '/');
       this.species     = this.speciesPath.split('/').pop();
       this.chr         = params[4];
       this.start       = parseInt(params[5], 10);
       this.end         = parseInt(params[6], 10);
       this.strand      = parseInt(params[7], 10);
       this.multi       = area.klass.multi ? n : false;
-      
       if (!this.speciesPath.match(/^\//)) {
         this.speciesPath = '/' + this.speciesPath;
       }
     }
-    
+
     area = null;
 
     delete this.areaCoords.a;
@@ -122,7 +120,7 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
 
     // The location parameter that is due to be changed has its value replaced with %s
     this.baseURL = window.location.href.replace(/&/g, ';').replace(/#.*$/g, '').replace(r, '$1%s;').replace(/[\?;]$/g, '');
-    
+
     // Add r parameter if it doesn't exist already
     if (!this.baseURL.match(/%s/)) {
       this.baseURL += (this.baseURL.match(/\?/) ? ';' : '?') + 'r=%s';
@@ -378,7 +376,7 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
     var scale        = (max - min + 1) / (this.areaCoords.r - this.areaCoords.l);
     var url          = this.baseURL;
     var menu, caption, start, end, tmp, cls;
-    
+
     // Gene, transcript views
     function notLocation() {
       var view = end - start + 1 > Ensembl.maxRegionLength ? 'Overview' : 'View';
@@ -405,7 +403,8 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
       var label  = start ? 'region' : 'location';
           label += panel.species === Ensembl.species ? '' : ' on ' + Ensembl.species.replace(/_/g, ' ');
 
-      menu    = [ '<a href="' + url.replace(/%s/, Ensembl.coreParams.r + ';align_start=' + start + ';align_end=' + end) + '">Jump to best aligned ' + label + '</a>' ];
+      menu    = [ '<a class="loc-icon-a" href="' + url.replace(/%s/, Ensembl.coreParams.r + ';align_start=' + start + ';align_end=' + end) + 
+                  '"><span class="loc-icon loc-change"></span>Jump to best aligned ' + label + '</a>' ];
       caption = 'Alignment: ' + (start ? start + '-' + end : panel.location);
     }
 
@@ -432,13 +431,12 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
         start = this.end + this.start - end;
         end   = this.end + this.start - tmp;
       }
-      
-      if (this.align === true) {
+
+      if (this.align) {
         align();
       } else {
         url     = url.replace(/%s/, this.chr + ':' + start + '-' + end);
         caption = 'Region: ' + this.chr + ':' + start + '-' + end;
-        
         if (!locationView) {
           notLocation();
         } else if (this.multi !== false) {
@@ -457,14 +455,15 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
         }
       }
 
-      if (this.multi === false) {
-        menu.unshift('<a class="_location_mark loc-icon-a" href="' + Ensembl.updateURL({mr: this.chr + ':' + start + '-' + end}, window.location.href) + '"><span class="loc-icon loc-mark"></span>Mark region (' + (end - start + 1) + ' bp)</a>');
+      if (this.multi === false && !this.align) {
+        var no_bases  =  ' (' + (end - start + 1) + ' bp)';
+        menu.unshift('<a class="_location_mark loc-icon-a" href="' +  '"><span class="loc-icon loc-mark"></span>Mark region' + no_bases + '</a>');
       }
 
     } else { // Point select
       this.location = Math.floor(min + (this.coords.x - this.areaCoords.l) * scale);
 
-      if (this.align === true) {
+      if (this.align) {
         url = this.zoomURL(1/10);
         align();
       } else {
@@ -608,7 +607,7 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
       start = this.start;
     }
 
-    if (this.align === true) {
+    if (this.align) {
       return this.baseURL.replace(/%s/, Ensembl.coreParams.r + ';align_start=' + start + ';align_end=' + end);
     } else {
       return this.baseURL.replace(/%s/, (this.chr || Ensembl.location.name) + ':' + start + '-' + end);
@@ -652,7 +651,6 @@ Ensembl.Panel.ZMenu = Ensembl.Panel.extend({
   showExisting: function (data) {
     this.event  = data.event;
     this.coords = data.coords;
-    
     if (this.group || this.drag || this.event.shiftKey) {
       if (this.elLk.header) {
         this.elLk.header.remove();

modules/EnsEMBL/Web/Factory/MultipleLocation.pm

@@ -286,13 +286,11 @@ sub best_guess {
   my ($self, $slice, $id, $species, $seq_region_name) = @_;
 
   my $width = $slice->end - $slice->start + 1;
-  my $production_species = $self->species_defs->get_config($species, 'SPECIES_PRODUCTION_NAME');
-  
-  foreach my $method ($seq_region_name && $species eq $self->species ? 'LASTZ_PATCH' : (), qw(BLASTZ_NET LASTZ_NET TRANSLATED_BLAT TRANSLATED_BLAT_NET BLASTZ_RAW LASTZ_RAW BLASTZ_CHAIN)) {
-    my ($seq_region, $cp, $strand);
+
+  foreach my $method ($seq_region_name && $species eq $self->species ? 'LASTZ_PATCH' : (), qw(BLASTZ_NET LASTZ_NET TRANSLATED_BLAT TRANSLATED_BLAT_NET BLASTZ_RAW LASTZ_RAW BLASTZ_CHAIN CACTUS_HAL_PW)) {    my ($seq_region, $cp, $strand);
 
     eval {
-      ($seq_region, $cp, $strand) = $self->dna_align_feature_adaptor->interpolate_best_location($slice, $production_species, $method, $seq_region_name);
+      ($seq_region, $cp, $strand) = $self->dna_align_feature_adaptor->interpolate_best_location($slice, $species, $method, $seq_region_name);
     };
 
     if ($seq_region) {

modules/EnsEMBL/Web/ZMenu/Contig.pm

@@ -33,18 +33,19 @@ sub content {
   my $slice_type      = $slice->coord_system_name;
   my $top_level_slice = $slice->project('toplevel')->[0]->to_Slice;
   my $action          = $slice->length > $threshold ? 'Overview' : 'View';
-  
+
   $self->caption($slice_name);
 
   $self->add_entry({
     label => "Centre on $slice_type $slice_name",
     link  => $hub->url({ 
       type   => 'Location', 
       action => $action, 
-      region => $slice_name 
+      region => $slice_name,
+      r => sprintf '%s:%s-%s', map $top_level_slice->$_, qw(seq_region_name start end)
     })
   });
-  
+
   $self->add_entry({
     label      => "Export $slice_type sequence/features",
     link_class => 'modal_link',
@@ -55,7 +56,7 @@ sub content {
       r        => sprintf '%s:%s-%s', map $top_level_slice->$_, qw(seq_region_name start end)
     })
   });
-  
+
   foreach my $cs (@{$db_adaptor->get_CoordSystemAdaptor->fetch_all || []}) {
     next if $cs->name eq $slice_type;  # don't show the slice coord system twice
     next if $cs->name eq 'chromosome'; # don't allow breaking of site by exporting all chromosome features
@@ -77,7 +78,9 @@ sub content {
       link  => $hub->url({
         type   => 'Location', 
         action => $action, 
-        region => $new_slice_name
+        region => $new_slice_name,
+        r => sprintf '%s:%s-%s', map $new_slice->$_, qw(seq_region_name start end)
+
       })
     });